pileup_freqs: Create a table of A,C,G,T nucleotide frequencies for pileup...
In lixiangchun/lxctk: Li Xiangchun's tool-kit (lxctk)

Description Usage Arguments Value See Also Examples

Create a table of A,C,G,T nucleotide frequencies for pileup result. Source code from: https://seqqc.wordpress.com/2015/03/10/calculate-nucelotide-frequency-with-rsamtools-pileup/

1	pileup_freqs(plp)

plp

Pileup result returned by Rsamtools::pileup(...).

A data frame (or list, need to check by yourself) of A,C,G,T nucleotide frequencies.

calc_allelic_freqs

library(Rsamtools)

# 1. Not run:
plp <- Rsamtools::pileup(...)

# 2. Not run -  computing the allelic counts for several SNPs
library(VariantAnnotation)

bamfile <- 'Tumor.rmdup.bam'
bf <- BamFile(bamfile)

#read list of SNPs (several)
vcf <- readVcf("vcfExample_chr17.vcf", "hg19")
vcf.ranges <- rowData(vcf) # You can also create a list of SNPs with GRanges

#compute pileup
#param <- ScanBamParam(which=GRanges("chr17",IRanges(start=685640, end=685650)))
param <- ScanBamParam(which=vcf.ranges)

p_param <- PileupParam(max_depth=1000, ignore_query_Ns=FALSE)
plp <- pileup(bf, scanBamParam=param, pileupParam=p_param)
dim(plp)

#create table of nucleotide frequencies
pileup_freqs(plp)

close(bf)